In ergm_model() documentation, ergm_preprocess_response() usage is no…

…w explained. fixes #459
statnet · May 27, 2022 · 4e2ab11 · 4e2ab11
1 parent 69ca4eb
commit 4e2ab11
Show file tree

Hide file tree

Showing 68 changed files with 74 additions and 6 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: ergm
-Version: 4.2-6930
-Date: 2022-05-26
+Version: 4.2-6932
+Date: 2022-05-27
 Title: Fit, Simulate and Diagnose Exponential-Family Models for Networks
 Authors@R: c(
              person("Mark S.", "Handcock", role=c("aut"), email="[email protected]"),

diff --git a/R/ergm_model.R b/R/ergm_model.R
@@ -24,7 +24,7 @@
 #' @param formula An [ergm()]
 #' formula of the form \code{network ~ model.term(s)} or \code{~
 #' model.term(s)}.
-#' @param nw The network of interest; if passed, the LHS of `formula` is ignored. This is the recommended usage.
+#' @param nw The network of interest, optionally instrumented with [ergm_preprocess_response()] to have a response attribute specification; if passed, the LHS of `formula` is ignored. This is the recommended usage.
 #' @param silent logical, whether to print the warning messages from the
 #' initialization of each model term.
 #' @param \dots additional parameters for model formulation
@@ -33,13 +33,14 @@
 #' @param env a throwaway argument needed to prevent conflicts with some usages of `ergm_model`. The initialization environment is *always* taken from the `formula`.
 #' @param offset.decorate logical; whether offset coefficient and parameter names should be enclosed in `"offset()"`. 
 #' @param object An `ergm_model` object.
+#' @note Earlier versions also had an optional `response=` parameter that, if not `NULL`, switched to valued mode and used the edge attribute named in `response=` as the response. This is no longer used; instead, the response is to be set on `nw` via `ergm_preprocess_response(nw, response)`.
 #' @return `ergm_model` returns an  `ergm_model` object as a list
 #' containing:
 #' \item{terms}{a list of terms and 'term components' initialized by the
 #' appropriate \code{InitErgmTerm.X} function.}
 #' \item{etamap}{the theta -> eta mapping as a list returned from
 #' <ergm.etamap>}
-#' @seealso [summary.ergm_model()]
+#' @seealso [summary.ergm_model()], [ergm_preprocess_response()]
 #' @keywords internal
 #' @export
 ergm_model <- function(formula, nw=NULL, silent=FALSE, ..., term.options=list(), extra.aux=list(), env=globalenv(), offset.decorate=TRUE){

diff --git a/man/ergm_model.Rd b/man/ergm_model.Rd
diff --git a/tests/testthat/test-C-curved.R b/tests/testthat/test-C-curved.R
@@ -1,3 +1,4 @@
+library(testthat); library(ergm)
 #  File tests/testthat/test-C-curved.R in package ergm, part of the
 #  Statnet suite of packages for network analysis, https://statnet.org .
 #

diff --git a/tests/testthat/test-Sum.R b/tests/testthat/test-Sum.R
@@ -1,3 +1,4 @@
+library(testthat); library(ergm)
 #  File tests/testthat/test-Sum.R in package ergm, part of the
 #  Statnet suite of packages for network analysis, https://statnet.org .
 #

diff --git a/tests/testthat/test-bd.R b/tests/testthat/test-bd.R
@@ -1,3 +1,4 @@
+library(testthat); library(ergm)
 #  File tests/testthat/test-bd.R in package ergm, part of the
 #  Statnet suite of packages for network analysis, https://statnet.org .
 #

diff --git a/tests/testthat/test-bipartite-missing-data.R b/tests/testthat/test-bipartite-missing-data.R
@@ -1,3 +1,4 @@
+library(testthat); library(ergm)
 #  File tests/testthat/test-bipartite-missing-data.R in package ergm, part of the
 #  Statnet suite of packages for network analysis, https://statnet.org .
 #

diff --git a/tests/testthat/test-bridge-target.stats.R b/tests/testthat/test-bridge-target.stats.R
@@ -1,3 +1,4 @@
+library(testthat); library(ergm)
 #  File tests/testthat/test-bridge-target.stats.R in package ergm, part of the
 #  Statnet suite of packages for network analysis, https://statnet.org .
 #

diff --git a/tests/testthat/test-c-ergm_model.R b/tests/testthat/test-c-ergm_model.R
@@ -1,3 +1,4 @@
+library(testthat); library(ergm)
 #  File tests/testthat/test-c-ergm_model.R in package ergm, part of the
 #  Statnet suite of packages for network analysis, https://statnet.org .
 #

diff --git a/tests/testthat/test-checkpointing.R b/tests/testthat/test-checkpointing.R
@@ -1,3 +1,4 @@
+library(testthat); library(ergm)
 #  File tests/testthat/test-checkpointing.R in package ergm, part of the
 #  Statnet suite of packages for network analysis, https://statnet.org .
 #

diff --git a/tests/testthat/test-constrain-blockdiag.R b/tests/testthat/test-constrain-blockdiag.R
@@ -1,3 +1,4 @@
+library(testthat); library(ergm)
 #  File tests/testthat/test-constrain-blockdiag.R in package ergm, part of the
 #  Statnet suite of packages for network analysis, https://statnet.org .
 #

diff --git a/tests/testthat/test-constrain-degrees-edges.R b/tests/testthat/test-constrain-degrees-edges.R
@@ -1,3 +1,4 @@
+library(testthat); library(ergm)
 #  File tests/testthat/test-constrain-degrees-edges.R in package ergm, part of the
 #  Statnet suite of packages for network analysis, https://statnet.org .
 #

diff --git a/tests/testthat/test-constrain-dind.R b/tests/testthat/test-constrain-dind.R
@@ -1,3 +1,4 @@
+library(testthat); library(ergm)
 #  File tests/testthat/test-constrain-dind.R in package ergm, part of the
 #  Statnet suite of packages for network analysis, https://statnet.org .
 #

diff --git a/tests/testthat/test-constrain-egocentric.R b/tests/testthat/test-constrain-egocentric.R
@@ -1,3 +1,4 @@
+library(testthat); library(ergm)
 #  File tests/testthat/test-constrain-egocentric.R in package ergm, part of the
 #  Statnet suite of packages for network analysis, https://statnet.org .
 #

diff --git a/tests/testthat/test-constraints.R b/tests/testthat/test-constraints.R
@@ -1,3 +1,4 @@
+library(testthat); library(ergm)
 #  File tests/testthat/test-constraints.R in package ergm, part of the
 #  Statnet suite of packages for network analysis, https://statnet.org .
 #

diff --git a/tests/testthat/test-drop.R b/tests/testthat/test-drop.R
@@ -1,3 +1,4 @@
+library(testthat); library(ergm)
 #  File tests/testthat/test-drop.R in package ergm, part of the
 #  Statnet suite of packages for network analysis, https://statnet.org .
 #

diff --git a/tests/testthat/test-ergm-godfather.R b/tests/testthat/test-ergm-godfather.R
@@ -1,3 +1,4 @@
+library(testthat); library(ergm)
 #  File tests/testthat/test-ergm-godfather.R in package ergm, part of the
 #  Statnet suite of packages for network analysis, https://statnet.org .
 #

diff --git a/tests/testthat/test-ergm-san.R b/tests/testthat/test-ergm-san.R
@@ -1,3 +1,4 @@
+library(testthat); library(ergm)
 #  File tests/testthat/test-ergm-san.R in package ergm, part of the
 #  Statnet suite of packages for network analysis, https://statnet.org .
 #

diff --git a/tests/testthat/test-ergm-term-doc.R b/tests/testthat/test-ergm-term-doc.R
@@ -1,3 +1,4 @@
+library(testthat); library(ergm)
 #  File tests/testthat/test-ergm-term-doc.R in package ergm, part of the
 #  Statnet suite of packages for network analysis, https://statnet.org .
 #

diff --git a/tests/testthat/test-ergm.bridge.llr.R b/tests/testthat/test-ergm.bridge.llr.R
@@ -1,3 +1,4 @@
+library(testthat); library(ergm)
 #  File tests/testthat/test-ergm.bridge.llr.R in package ergm, part of the
 #  Statnet suite of packages for network analysis, https://statnet.org .
 #

diff --git a/tests/testthat/test-ergmMPLE.R b/tests/testthat/test-ergmMPLE.R
@@ -1,3 +1,4 @@
+library(testthat); library(ergm)
 #  File tests/testthat/test-ergmMPLE.R in package ergm, part of the
 #  Statnet suite of packages for network analysis, https://statnet.org .
 #

diff --git a/tests/testthat/test-fix.curved.R b/tests/testthat/test-fix.curved.R
@@ -1,3 +1,4 @@
+library(testthat); library(ergm)
 #  File tests/testthat/test-fix.curved.R in package ergm, part of the
 #  Statnet suite of packages for network analysis, https://statnet.org .
 #

diff --git a/tests/testthat/test-gflomiss.R b/tests/testthat/test-gflomiss.R
@@ -1,3 +1,4 @@
+library(testthat); library(ergm)
 #  File tests/testthat/test-gflomiss.R in package ergm, part of the
 #  Statnet suite of packages for network analysis, https://statnet.org .
 #

diff --git a/tests/testthat/test-gmonkmiss.R b/tests/testthat/test-gmonkmiss.R
@@ -1,3 +1,4 @@
+library(testthat); library(ergm)
 #  File tests/testthat/test-gmonkmiss.R in package ergm, part of the
 #  Statnet suite of packages for network analysis, https://statnet.org .
 #

diff --git a/tests/testthat/test-gof.R b/tests/testthat/test-gof.R
@@ -1,3 +1,4 @@
+library(testthat); library(ergm)
 #  File tests/testthat/test-gof.R in package ergm, part of the
 #  Statnet suite of packages for network analysis, https://statnet.org .
 #

diff --git a/tests/testthat/test-gw-sp.R b/tests/testthat/test-gw-sp.R
@@ -1,3 +1,4 @@
+library(testthat); library(ergm)
 #  File tests/testthat/test-gw-sp.R in package ergm, part of the
 #  Statnet suite of packages for network analysis, https://statnet.org .
 #

diff --git a/tests/testthat/test-metrics.R b/tests/testthat/test-metrics.R
@@ -1,3 +1,4 @@
+library(testthat); library(ergm)
 #  File tests/testthat/test-metrics.R in package ergm, part of the
 #  Statnet suite of packages for network analysis, https://statnet.org .
 #

diff --git a/tests/testthat/test-miss.CD.R b/tests/testthat/test-miss.CD.R
@@ -1,3 +1,4 @@
+library(testthat); library(ergm)
 #  File tests/testthat/test-miss.CD.R in package ergm, part of the
 #  Statnet suite of packages for network analysis, https://statnet.org .
 #

diff --git a/tests/testthat/test-miss.R b/tests/testthat/test-miss.R
@@ -1,3 +1,4 @@
+library(testthat); library(ergm)
 #  File tests/testthat/test-miss.R in package ergm, part of the
 #  Statnet suite of packages for network analysis, https://statnet.org .
 #

diff --git a/tests/testthat/test-mple-largenetwork.R b/tests/testthat/test-mple-largenetwork.R
@@ -1,3 +1,4 @@
+library(testthat); library(ergm)
 #  File tests/testthat/test-mple-largenetwork.R in package ergm, part of the
 #  Statnet suite of packages for network analysis, https://statnet.org .
 #

diff --git a/tests/testthat/test-mple-offset.R b/tests/testthat/test-mple-offset.R
@@ -1,3 +1,4 @@
+library(testthat); library(ergm)
 #  File tests/testthat/test-mple-offset.R in package ergm, part of the
 #  Statnet suite of packages for network analysis, https://statnet.org .
 #

diff --git a/tests/testthat/test-mple-target.R b/tests/testthat/test-mple-target.R
@@ -1,3 +1,4 @@
+library(testthat); library(ergm)
 #  File tests/testthat/test-mple-target.R in package ergm, part of the
 #  Statnet suite of packages for network analysis, https://statnet.org .
 #

diff --git a/tests/testthat/test-nodemix.R b/tests/testthat/test-nodemix.R
@@ -1,3 +1,4 @@
+library(testthat); library(ergm)
 #  File tests/testthat/test-nodemix.R in package ergm, part of the
 #  Statnet suite of packages for network analysis, https://statnet.org .
 #

diff --git a/tests/testthat/test-nodrop.R b/tests/testthat/test-nodrop.R
@@ -1,3 +1,4 @@
+library(testthat); library(ergm)
 #  File tests/testthat/test-nodrop.R in package ergm, part of the
 #  Statnet suite of packages for network analysis, https://statnet.org .
 #

diff --git a/tests/testthat/test-nonident-test.R b/tests/testthat/test-nonident-test.R
@@ -1,3 +1,4 @@
+library(testthat); library(ergm)
 #  File tests/testthat/test-nonident-test.R in package ergm, part of the
 #  Statnet suite of packages for network analysis, https://statnet.org .
 #

diff --git a/tests/testthat/test-nonunique-names.R b/tests/testthat/test-nonunique-names.R
@@ -1,3 +1,4 @@
+library(testthat); library(ergm)
 #  File tests/testthat/test-nonunique-names.R in package ergm, part of the
 #  Statnet suite of packages for network analysis, https://statnet.org .
 #

diff --git a/tests/testthat/test-offsets.R b/tests/testthat/test-offsets.R
@@ -1,3 +1,4 @@
+library(testthat); library(ergm)
 #  File tests/testthat/test-offsets.R in package ergm, part of the
 #  Statnet suite of packages for network analysis, https://statnet.org .
 #

diff --git a/tests/testthat/test-operators.R b/tests/testthat/test-operators.R
@@ -1,3 +1,4 @@
+library(testthat); library(ergm)
 #  File tests/testthat/test-operators.R in package ergm, part of the
 #  Statnet suite of packages for network analysis, https://statnet.org .
 #

diff --git a/tests/testthat/test-parallel.R b/tests/testthat/test-parallel.R
@@ -1,3 +1,4 @@
+library(testthat); library(ergm)
 #  File tests/testthat/test-parallel.R in package ergm, part of the
 #  Statnet suite of packages for network analysis, https://statnet.org .
 #

diff --git a/tests/testthat/test-predict.ergm.R b/tests/testthat/test-predict.ergm.R
@@ -1,3 +1,4 @@
+library(testthat); library(ergm)
 #  File tests/testthat/test-predict.ergm.R in package ergm, part of the
 #  Statnet suite of packages for network analysis, https://statnet.org .
 #

diff --git a/tests/testthat/test-proposal-bdstrattnt.R b/tests/testthat/test-proposal-bdstrattnt.R
@@ -1,3 +1,4 @@
+library(testthat); library(ergm)
 #  File tests/testthat/test-proposal-bdstrattnt.R in package ergm, part of the
 #  Statnet suite of packages for network analysis, https://statnet.org .
 #

diff --git a/tests/testthat/test-runtime-diags.R b/tests/testthat/test-runtime-diags.R
@@ -1,3 +1,4 @@
+library(testthat); library(ergm)
 #  File tests/testthat/test-runtime-diags.R in package ergm, part of the
 #  Statnet suite of packages for network analysis, https://statnet.org .
 #

diff --git a/tests/testthat/test-scoping.R b/tests/testthat/test-scoping.R
@@ -1,3 +1,4 @@
+library(testthat); library(ergm)
 #  File tests/testthat/test-scoping.R in package ergm, part of the
 #  Statnet suite of packages for network analysis, https://statnet.org .
 #

diff --git a/tests/testthat/test-shrink-into-CH.R b/tests/testthat/test-shrink-into-CH.R
@@ -1,3 +1,4 @@
+library(testthat); library(ergm)
 #  File tests/testthat/test-shrink-into-CH.R in package ergm, part of the
 #  Statnet suite of packages for network analysis, https://statnet.org .
 #

diff --git a/tests/testthat/test-simple.R b/tests/testthat/test-simple.R
@@ -1,3 +1,4 @@
+library(testthat); library(ergm)
 #  File tests/testthat/test-simple.R in package ergm, part of the
 #  Statnet suite of packages for network analysis, https://statnet.org .
 #

diff --git a/tests/testthat/test-simulate-batch.R b/tests/testthat/test-simulate-batch.R
@@ -1,3 +1,4 @@
+library(testthat); library(ergm)
 #  File tests/testthat/test-simulate-batch.R in package ergm, part of the
 #  Statnet suite of packages for network analysis, https://statnet.org .
 #

diff --git a/tests/testthat/test-snctrl.R b/tests/testthat/test-snctrl.R
@@ -1,3 +1,4 @@
+library(testthat); library(ergm)
 #  File tests/testthat/test-snctrl.R in package ergm, part of the
 #  Statnet suite of packages for network analysis, https://statnet.org .
 #

diff --git a/tests/testthat/test-stocapprox.R b/tests/testthat/test-stocapprox.R
@@ -1,3 +1,4 @@
+library(testthat); library(ergm)
 #  File tests/testthat/test-stocapprox.R in package ergm, part of the
 #  Statnet suite of packages for network analysis, https://statnet.org .
 #

diff --git a/tests/testthat/test-target-offset.R b/tests/testthat/test-target-offset.R
@@ -1,3 +1,4 @@
+library(testthat); library(ergm)
 #  File tests/testthat/test-target-offset.R in package ergm, part of the
 #  Statnet suite of packages for network analysis, https://statnet.org .
 #

diff --git a/tests/testthat/test-term-Offset.R b/tests/testthat/test-term-Offset.R
@@ -1,3 +1,4 @@
+library(testthat); library(ergm)
 #  File tests/testthat/test-term-Offset.R in package ergm, part of the
 #  Statnet suite of packages for network analysis, https://statnet.org .
 #

diff --git a/tests/testthat/test-term-attrcov.R b/tests/testthat/test-term-attrcov.R
@@ -1,3 +1,4 @@
+library(testthat); library(ergm)
 #  File tests/testthat/test-term-attrcov.R in package ergm, part of the
 #  Statnet suite of packages for network analysis, https://statnet.org .
 #

diff --git a/tests/testthat/test-term-b12factor.R b/tests/testthat/test-term-b12factor.R
@@ -1,3 +1,4 @@
+library(testthat); library(ergm)
 #  File tests/testthat/test-term-b12factor.R in package ergm, part of the
 #  Statnet suite of packages for network analysis, https://statnet.org .
 #

diff --git a/tests/testthat/test-term-b12nodematch.R b/tests/testthat/test-term-b12nodematch.R
@@ -1,3 +1,4 @@
+library(testthat); library(ergm)
 #  File tests/testthat/test-term-b12nodematch.R in package ergm, part of the
 #  Statnet suite of packages for network analysis, https://statnet.org .
 #

diff --git a/tests/testthat/test-term-bipartite.R b/tests/testthat/test-term-bipartite.R
@@ -1,3 +1,4 @@
+library(testthat); library(ergm)
 #  File tests/testthat/test-term-bipartite.R in package ergm, part of the
 #  Statnet suite of packages for network analysis, https://statnet.org .
 #

diff --git a/tests/testthat/test-term-directed.R b/tests/testthat/test-term-directed.R
@@ -1,3 +1,4 @@
+library(testthat); library(ergm)
 #  File tests/testthat/test-term-directed.R in package ergm, part of the
 #  Statnet suite of packages for network analysis, https://statnet.org .
 #

diff --git a/tests/testthat/test-term-edgecov.R b/tests/testthat/test-term-edgecov.R
@@ -1,3 +1,4 @@
+library(testthat); library(ergm)
 #  File tests/testthat/test-term-edgecov.R in package ergm, part of the
 #  Statnet suite of packages for network analysis, https://statnet.org .
 #

diff --git a/tests/testthat/test-term-errors.R b/tests/testthat/test-term-errors.R
@@ -1,3 +1,4 @@
+library(testthat); library(ergm)
 #  File tests/testthat/test-term-errors.R in package ergm, part of the
 #  Statnet suite of packages for network analysis, https://statnet.org .
 #

diff --git a/tests/testthat/test-term-flexible.R b/tests/testthat/test-term-flexible.R
@@ -1,3 +1,4 @@
+library(testthat); library(ergm)
 #  File tests/testthat/test-term-flexible.R in package ergm, part of the
 #  Statnet suite of packages for network analysis, https://statnet.org .
 #

diff --git a/tests/testthat/test-term-hamming.R b/tests/testthat/test-term-hamming.R
@@ -1,3 +1,4 @@
+library(testthat); library(ergm)
 #  File tests/testthat/test-term-hamming.R in package ergm, part of the
 #  Statnet suite of packages for network analysis, https://statnet.org .
 #

diff --git a/tests/testthat/test-term-mm.R b/tests/testthat/test-term-mm.R
@@ -1,3 +1,4 @@
+library(testthat); library(ergm)
 #  File tests/testthat/test-term-mm.R in package ergm, part of the
 #  Statnet suite of packages for network analysis, https://statnet.org .
 #

diff --git a/tests/testthat/test-term-options.R b/tests/testthat/test-term-options.R
@@ -1,3 +1,4 @@
+library(testthat); library(ergm)
 #  File tests/testthat/test-term-options.R in package ergm, part of the
 #  Statnet suite of packages for network analysis, https://statnet.org .
 #

diff --git a/tests/testthat/test-term-undirected.R b/tests/testthat/test-term-undirected.R
@@ -1,3 +1,4 @@
+library(testthat); library(ergm)
 #  File tests/testthat/test-term-undirected.R in package ergm, part of the
 #  Statnet suite of packages for network analysis, https://statnet.org .
 #

diff --git a/tests/testthat/test-term-valued.R b/tests/testthat/test-term-valued.R
@@ -1,3 +1,4 @@
+library(testthat); library(ergm)
 #  File tests/testthat/test-term-valued.R in package ergm, part of the
 #  Statnet suite of packages for network analysis, https://statnet.org .
 #

diff --git a/tests/testthat/test-u-function.R b/tests/testthat/test-u-function.R
@@ -1,3 +1,4 @@
+library(testthat); library(ergm)
 #  File tests/testthat/test-u-function.R in package ergm, part of the
 #  Statnet suite of packages for network analysis, https://statnet.org .
 #

diff --git a/tests/testthat/test-update.network.R b/tests/testthat/test-update.network.R
@@ -1,3 +1,4 @@
+library(testthat); library(ergm)
 #  File tests/testthat/test-update.network.R in package ergm, part of the
 #  Statnet suite of packages for network analysis, https://statnet.org .
 #

diff --git a/tests/testthat/test-valued-sim.R b/tests/testthat/test-valued-sim.R
@@ -1,3 +1,4 @@
+library(testthat); library(ergm)
 #  File tests/testthat/test-valued-sim.R in package ergm, part of the
 #  Statnet suite of packages for network analysis, https://statnet.org .
 #

diff --git a/tests/testthat/test-valued-terms.R b/tests/testthat/test-valued-terms.R
@@ -1,3 +1,4 @@
+library(testthat); library(ergm)
 #  File tests/testthat/test-valued-terms.R in package ergm, part of the
 #  Statnet suite of packages for network analysis, https://statnet.org .
 #

diff --git a/tests/testthat/test-weighted-population.R b/tests/testthat/test-weighted-population.R
@@ -1,3 +1,4 @@
+library(testthat); library(ergm)
 #  File tests/testthat/test-weighted-population.R in package ergm, part of the
 #  Statnet suite of packages for network analysis, https://statnet.org .
 #